Starting phenix.real_space_refine on Fri Aug 9 10:21:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u7k_20672/08_2024/6u7k_20672_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u7k_20672/08_2024/6u7k_20672.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u7k_20672/08_2024/6u7k_20672.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u7k_20672/08_2024/6u7k_20672.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u7k_20672/08_2024/6u7k_20672_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u7k_20672/08_2024/6u7k_20672_neut.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 16191 2.51 5 N 4029 2.21 5 O 5187 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 365": "OE1" <-> "OE2" Residue "A ARG 544": "NH1" <-> "NH2" Residue "A GLU 623": "OE1" <-> "OE2" Residue "A PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 727": "OE1" <-> "OE2" Residue "A GLU 844": "OE1" <-> "OE2" Residue "A GLU 853": "OE1" <-> "OE2" Residue "A PHE 864": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 921": "NH1" <-> "NH2" Residue "A GLU 945": "OE1" <-> "OE2" Residue "A GLU 1012": "OE1" <-> "OE2" Residue "A GLU 1016": "OE1" <-> "OE2" Residue "A GLU 1104": "OE1" <-> "OE2" Residue "A ARG 1126": "NH1" <-> "NH2" Residue "A GLU 1174": "OE1" <-> "OE2" Residue "A GLU 1190": "OE1" <-> "OE2" Residue "A GLU 1198": "OE1" <-> "OE2" Residue "A PHE 1217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1221": "OE1" <-> "OE2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 365": "OE1" <-> "OE2" Residue "B ARG 544": "NH1" <-> "NH2" Residue "B PHE 585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 623": "OE1" <-> "OE2" Residue "B TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 727": "OE1" <-> "OE2" Residue "B GLU 853": "OE1" <-> "OE2" Residue "B ARG 921": "NH1" <-> "NH2" Residue "B ASP 925": "OD1" <-> "OD2" Residue "B GLU 945": "OE1" <-> "OE2" Residue "B GLU 1012": "OE1" <-> "OE2" Residue "B GLU 1016": "OE1" <-> "OE2" Residue "B ARG 1126": "NH1" <-> "NH2" Residue "B GLU 1174": "OE1" <-> "OE2" Residue "B GLU 1190": "OE1" <-> "OE2" Residue "B GLU 1198": "OE1" <-> "OE2" Residue "B GLU 1221": "OE1" <-> "OE2" Residue "C PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 314": "OE1" <-> "OE2" Residue "C PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 365": "OE1" <-> "OE2" Residue "C PHE 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 544": "NH1" <-> "NH2" Residue "C PHE 585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 623": "OE1" <-> "OE2" Residue "C TYR 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 727": "OE1" <-> "OE2" Residue "C GLU 853": "OE1" <-> "OE2" Residue "C GLU 854": "OE1" <-> "OE2" Residue "C ARG 921": "NH1" <-> "NH2" Residue "C GLU 945": "OE1" <-> "OE2" Residue "C GLU 1012": "OE1" <-> "OE2" Residue "C GLU 1016": "OE1" <-> "OE2" Residue "C ARG 1126": "NH1" <-> "NH2" Residue "C GLU 1174": "OE1" <-> "OE2" Residue "C GLU 1190": "OE1" <-> "OE2" Residue "C GLU 1198": "OE1" <-> "OE2" Residue "C GLU 1221": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 25515 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 8139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8139 Classifications: {'peptide': 1064} Link IDs: {'PTRANS': 36, 'TRANS': 1027} Chain breaks: 6 Chain: "B" Number of atoms: 8139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8139 Classifications: {'peptide': 1064} Link IDs: {'PTRANS': 36, 'TRANS': 1027} Chain breaks: 6 Chain: "C" Number of atoms: 8139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8139 Classifications: {'peptide': 1064} Link IDs: {'PTRANS': 36, 'TRANS': 1027} Chain breaks: 6 Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 17.12, per 1000 atoms: 0.67 Number of scatterers: 25515 At special positions: 0 Unit cell: (147.275, 155.875, 159.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 5187 8.00 N 4029 7.00 C 16191 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 231 " distance=2.02 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 304 " distance=2.06 Simple disulfide: pdb=" SG CYS A 346 " - pdb=" SG CYS A 370 " distance=2.03 Simple disulfide: pdb=" SG CYS A 461 " - pdb=" SG CYS A 470 " distance=2.01 Simple disulfide: pdb=" SG CYS A 540 " - pdb=" SG CYS A 586 " distance=2.04 Simple disulfide: pdb=" SG CYS A 569 " - pdb=" SG CYS A 596 " distance=2.01 Simple disulfide: pdb=" SG CYS A 646 " - pdb=" SG CYS A 697 " distance=2.04 Simple disulfide: pdb=" SG CYS A 741 " - pdb=" SG CYS A 754 " distance=2.04 Simple disulfide: pdb=" SG CYS A 805 " - pdb=" SG CYS A 827 " distance=2.04 Simple disulfide: pdb=" SG CYS A 810 " - pdb=" SG CYS A 816 " distance=2.04 Simple disulfide: pdb=" SG CYS A 917 " - pdb=" SG CYS A 928 " distance=2.05 Simple disulfide: pdb=" SG CYS A1119 " - pdb=" SG CYS A1130 " distance=1.99 Simple disulfide: pdb=" SG CYS A1170 " - pdb=" SG CYS A1223 " distance=2.03 Simple disulfide: pdb=" SG CYS B 227 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 304 " distance=2.01 Simple disulfide: pdb=" SG CYS B 346 " - pdb=" SG CYS B 370 " distance=2.03 Simple disulfide: pdb=" SG CYS B 461 " - pdb=" SG CYS B 470 " distance=2.00 Simple disulfide: pdb=" SG CYS B 540 " - pdb=" SG CYS B 586 " distance=2.04 Simple disulfide: pdb=" SG CYS B 569 " - pdb=" SG CYS B 596 " distance=2.00 Simple disulfide: pdb=" SG CYS B 646 " - pdb=" SG CYS B 697 " distance=2.03 Simple disulfide: pdb=" SG CYS B 741 " - pdb=" SG CYS B 754 " distance=2.00 Simple disulfide: pdb=" SG CYS B 805 " - pdb=" SG CYS B 827 " distance=2.04 Simple disulfide: pdb=" SG CYS B 810 " - pdb=" SG CYS B 816 " distance=2.10 Simple disulfide: pdb=" SG CYS B 917 " - pdb=" SG CYS B 928 " distance=2.05 Simple disulfide: pdb=" SG CYS B1119 " - pdb=" SG CYS B1130 " distance=1.99 Simple disulfide: pdb=" SG CYS B1170 " - pdb=" SG CYS B1223 " distance=2.04 Simple disulfide: pdb=" SG CYS C 227 " - pdb=" SG CYS C 231 " distance=2.02 Simple disulfide: pdb=" SG CYS C 280 " - pdb=" SG CYS C 304 " distance=2.02 Simple disulfide: pdb=" SG CYS C 346 " - pdb=" SG CYS C 370 " distance=2.05 Simple disulfide: pdb=" SG CYS C 461 " - pdb=" SG CYS C 470 " distance=2.00 Simple disulfide: pdb=" SG CYS C 540 " - pdb=" SG CYS C 586 " distance=2.04 Simple disulfide: pdb=" SG CYS C 569 " - pdb=" SG CYS C 596 " distance=2.03 Simple disulfide: pdb=" SG CYS C 646 " - pdb=" SG CYS C 697 " distance=2.03 Simple disulfide: pdb=" SG CYS C 741 " - pdb=" SG CYS C 754 " distance=2.03 Simple disulfide: pdb=" SG CYS C 805 " - pdb=" SG CYS C 827 " distance=2.03 Simple disulfide: pdb=" SG CYS C 810 " - pdb=" SG CYS C 816 " distance=2.04 Simple disulfide: pdb=" SG CYS C 917 " - pdb=" SG CYS C 928 " distance=2.01 Simple disulfide: pdb=" SG CYS C1119 " - pdb=" SG CYS C1130 " distance=2.00 Simple disulfide: pdb=" SG CYS C1170 " - pdb=" SG CYS C1223 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM24769 O5 NAG M 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM24953 O5 NAG R 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM24925 O5 NAG Q 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=3, symmetry=0 Links applied ALPHA1-2 " MAN D 4 " - " MAN D 5 " " MAN I 4 " - " MAN I 5 " " MAN N 4 " - " MAN N 5 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA I 3 " - " MAN I 4 " " BMA N 3 " - " MAN N 4 " ALPHA1-6 " BMA D 3 " - " MAN D 6 " " BMA I 3 " - " MAN I 6 " " BMA N 3 " - " MAN N 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1401 " - " ASN A 213 " " NAG A1408 " - " ASN A 297 " " NAG A1411 " - " ASN A 341 " " NAG A1412 " - " ASN A 348 " " NAG A1413 " - " ASN A 422 " " NAG A1416 " - " ASN A 553 " " NAG A1417 " - " ASN A 664 " " NAG A1420 " - " ASN A 723 " " NAG A1421 " - " ASN A 740 " " NAG A1422 " - " ASN A 778 " " NAG A1423 " - " ASN A 784 " " NAG A1426 " - " ASN A1006 " " NAG A1427 " - " ASN A1229 " " NAG B1401 " - " ASN B 213 " " NAG B1408 " - " ASN B 297 " " NAG B1411 " - " ASN B 341 " " NAG B1412 " - " ASN B 348 " " NAG B1413 " - " ASN B 422 " " NAG B1416 " - " ASN B 553 " " NAG B1417 " - " ASN B 664 " " NAG B1420 " - " ASN B 723 " " NAG B1421 " - " ASN B 740 " " NAG B1422 " - " ASN B 778 " " NAG B1423 " - " ASN B 784 " " NAG B1426 " - " ASN B1006 " " NAG B1427 " - " ASN B1229 " " NAG C1401 " - " ASN C 213 " " NAG C1408 " - " ASN C 297 " " NAG C1411 " - " ASN C 341 " " NAG C1412 " - " ASN C 348 " " NAG C1413 " - " ASN C 422 " " NAG C1416 " - " ASN C 553 " " NAG C1417 " - " ASN C 664 " " NAG C1420 " - " ASN C 723 " " NAG C1421 " - " ASN C 740 " " NAG C1422 " - " ASN C 778 " " NAG C1423 " - " ASN C 784 " " NAG C1426 " - " ASN C1006 " " NAG C1427 " - " ASN C1229 " " NAG D 1 " - " ASN A 261 " " NAG E 1 " - " ASN A 321 " " NAG F 1 " - " ASN A 511 " " NAG G 1 " - " ASN A 685 " " NAG H 1 " - " ASN A 870 " " NAG I 1 " - " ASN B 261 " " NAG J 1 " - " ASN B 321 " " NAG K 1 " - " ASN B 511 " " NAG L 1 " - " ASN B 685 " " NAG M 1 " - " ASN B 870 " " NAG N 1 " - " ASN C 261 " " NAG O 1 " - " ASN C 321 " " NAG P 1 " - " ASN C 511 " " NAG Q 1 " - " ASN C 685 " " NAG R 1 " - " ASN C 870 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.40 Conformation dependent library (CDL) restraints added in 5.2 seconds 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5934 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 43 sheets defined 23.8% alpha, 35.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.97 Creating SS restraints... Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 242 through 246 removed outlier: 4.239A pdb=" N HIS A 246 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 Processing helix chain 'A' and resid 463 through 470 Processing helix chain 'A' and resid 572 through 577 removed outlier: 3.694A pdb=" N ASN A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 811 Processing helix chain 'A' and resid 813 through 821 Processing helix chain 'A' and resid 827 through 849 removed outlier: 4.673A pdb=" N ALA A 833 " --> pdb=" O THR A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 860 removed outlier: 4.696A pdb=" N LEU A 858 " --> pdb=" O GLU A 854 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA A 859 " --> pdb=" O ALA A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 876 removed outlier: 4.220A pdb=" N GLY A 876 " --> pdb=" O THR A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 903 removed outlier: 3.640A pdb=" N VAL A 902 " --> pdb=" O LEU A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 933 removed outlier: 3.675A pdb=" N TYR A 931 " --> pdb=" O VAL A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 957 Processing helix chain 'A' and resid 970 through 981 removed outlier: 3.678A pdb=" N ALA A 974 " --> pdb=" O PRO A 970 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN A 976 " --> pdb=" O SER A 972 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A 981 " --> pdb=" O ALA A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1011 removed outlier: 3.905A pdb=" N SER A 999 " --> pdb=" O LEU A 995 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASN A1006 " --> pdb=" O SER A1002 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N SER A1009 " --> pdb=" O GLY A1005 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A1010 " --> pdb=" O ASN A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1018 Processing helix chain 'A' and resid 1019 through 1024 removed outlier: 3.647A pdb=" N GLY A1024 " --> pdb=" O THR A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1040 Processing helix chain 'A' and resid 1043 through 1052 removed outlier: 3.775A pdb=" N GLN A1052 " --> pdb=" O GLN A1048 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1055 No H-bonds generated for 'chain 'A' and resid 1053 through 1055' Processing helix chain 'A' and resid 1063 through 1068 Processing helix chain 'A' and resid 1072 through 1120 removed outlier: 4.293A pdb=" N VAL A1078 " --> pdb=" O LEU A1074 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG A1082 " --> pdb=" O VAL A1078 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A1083 " --> pdb=" O GLN A1079 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A1107 " --> pdb=" O THR A1103 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER A1108 " --> pdb=" O GLU A1104 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A1111 " --> pdb=" O ALA A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1239 removed outlier: 3.823A pdb=" N VAL A1238 " --> pdb=" O GLN A1234 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 235 removed outlier: 3.692A pdb=" N ALA B 235 " --> pdb=" O THR B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 246 removed outlier: 4.240A pdb=" N HIS B 246 " --> pdb=" O SER B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 326 removed outlier: 3.509A pdb=" N ILE B 326 " --> pdb=" O THR B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 473 removed outlier: 3.681A pdb=" N LEU B 468 " --> pdb=" O PRO B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 577 removed outlier: 3.654A pdb=" N ASN B 577 " --> pdb=" O LEU B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 804 through 811 Processing helix chain 'B' and resid 813 through 821 removed outlier: 3.723A pdb=" N GLN B 818 " --> pdb=" O SER B 814 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU B 819 " --> pdb=" O ARG B 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 847 removed outlier: 4.632A pdb=" N ALA B 833 " --> pdb=" O THR B 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 860 removed outlier: 3.509A pdb=" N GLN B 857 " --> pdb=" O GLU B 853 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU B 858 " --> pdb=" O GLU B 854 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA B 859 " --> pdb=" O ALA B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 871 through 876 removed outlier: 4.258A pdb=" N GLY B 876 " --> pdb=" O THR B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 892 through 904 removed outlier: 3.990A pdb=" N VAL B 902 " --> pdb=" O LEU B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 919 removed outlier: 3.984A pdb=" N SER B 918 " --> pdb=" O TYR B 914 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ASN B 919 " --> pdb=" O LYS B 915 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 914 through 919' Processing helix chain 'B' and resid 925 through 933 removed outlier: 3.837A pdb=" N TYR B 931 " --> pdb=" O VAL B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 943 through 957 Processing helix chain 'B' and resid 970 through 981 removed outlier: 3.510A pdb=" N ALA B 974 " --> pdb=" O PRO B 970 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN B 976 " --> pdb=" O SER B 972 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR B 981 " --> pdb=" O ALA B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1009 removed outlier: 3.860A pdb=" N SER B1002 " --> pdb=" O GLU B 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 1014 through 1018 Processing helix chain 'B' and resid 1019 through 1024 removed outlier: 3.585A pdb=" N GLY B1024 " --> pdb=" O THR B1021 " (cutoff:3.500A) Processing helix chain 'B' and resid 1027 through 1041 Processing helix chain 'B' and resid 1043 through 1052 removed outlier: 3.587A pdb=" N LEU B1049 " --> pdb=" O ALA B1045 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN B1052 " --> pdb=" O GLN B1048 " (cutoff:3.500A) Processing helix chain 'B' and resid 1063 through 1070 Processing helix chain 'B' and resid 1072 through 1120 removed outlier: 3.850A pdb=" N ASP B1077 " --> pdb=" O ILE B1073 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL B1078 " --> pdb=" O LEU B1074 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG B1082 " --> pdb=" O VAL B1078 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA B1107 " --> pdb=" O THR B1103 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER B1108 " --> pdb=" O GLU B1104 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU B1111 " --> pdb=" O ALA B1107 " (cutoff:3.500A) Processing helix chain 'B' and resid 1234 through 1239 removed outlier: 3.825A pdb=" N VAL B1238 " --> pdb=" O GLN B1234 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 326 Processing helix chain 'C' and resid 463 through 472 removed outlier: 3.822A pdb=" N LEU C 468 " --> pdb=" O PRO C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 577 removed outlier: 3.679A pdb=" N ASN C 577 " --> pdb=" O LEU C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 811 Processing helix chain 'C' and resid 813 through 821 Processing helix chain 'C' and resid 825 through 849 removed outlier: 4.351A pdb=" N ALA C 833 " --> pdb=" O THR C 829 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 860 removed outlier: 4.912A pdb=" N LEU C 858 " --> pdb=" O GLU C 854 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA C 859 " --> pdb=" O ALA C 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 871 through 876 removed outlier: 4.421A pdb=" N GLY C 876 " --> pdb=" O THR C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 892 through 901 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.903A pdb=" N ARG C 916 " --> pdb=" O ASP C 913 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N SER C 918 " --> pdb=" O LYS C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 933 removed outlier: 4.132A pdb=" N TYR C 931 " --> pdb=" O VAL C 927 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 956 Processing helix chain 'C' and resid 957 through 960 Processing helix chain 'C' and resid 970 through 981 removed outlier: 3.609A pdb=" N ALA C 974 " --> pdb=" O PRO C 970 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR C 981 " --> pdb=" O ALA C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 991 through 1009 Processing helix chain 'C' and resid 1014 through 1018 Processing helix chain 'C' and resid 1019 through 1024 removed outlier: 3.703A pdb=" N GLY C1024 " --> pdb=" O THR C1021 " (cutoff:3.500A) Processing helix chain 'C' and resid 1027 through 1042 Processing helix chain 'C' and resid 1043 through 1052 removed outlier: 3.575A pdb=" N GLN C1052 " --> pdb=" O GLN C1048 " (cutoff:3.500A) Processing helix chain 'C' and resid 1063 through 1069 Processing helix chain 'C' and resid 1072 through 1119 removed outlier: 3.524A pdb=" N ASP C1077 " --> pdb=" O ILE C1073 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C1078 " --> pdb=" O LEU C1074 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG C1082 " --> pdb=" O VAL C1078 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA C1107 " --> pdb=" O THR C1103 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER C1108 " --> pdb=" O GLU C1104 " (cutoff:3.500A) Processing helix chain 'C' and resid 1234 through 1239 removed outlier: 3.529A pdb=" N VAL C1238 " --> pdb=" O GLN C1234 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 51 removed outlier: 4.262A pdb=" N TYR A 209 " --> pdb=" O CYS A 227 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TYR A 223 " --> pdb=" O ASN A 213 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 177 through 181 removed outlier: 3.504A pdb=" N GLY A 75 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 268 through 285 removed outlier: 3.544A pdb=" N LEU A 276 " --> pdb=" O ASN A 442 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASN A 442 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL A 278 " --> pdb=" O SER A 440 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N SER A 440 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N CYS A 280 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE A 438 " --> pdb=" O CYS A 280 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU A 282 " --> pdb=" O TRP A 436 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N TRP A 436 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR A 437 " --> pdb=" O ASN A 319 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL A 403 " --> pdb=" O TYR A 410 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 268 through 285 removed outlier: 3.544A pdb=" N LEU A 276 " --> pdb=" O ASN A 442 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASN A 442 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL A 278 " --> pdb=" O SER A 440 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N SER A 440 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N CYS A 280 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE A 438 " --> pdb=" O CYS A 280 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU A 282 " --> pdb=" O TRP A 436 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N TRP A 436 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ASP A 445 " --> pdb=" O TYR A 460 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N TYR A 460 " --> pdb=" O ASP A 445 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU A 447 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE A 458 " --> pdb=" O LEU A 447 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLU A 449 " --> pdb=" O GLN A 456 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 291 through 295 removed outlier: 3.548A pdb=" N GLN A 292 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA A 418 " --> pdb=" O HIS A 335 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE A 332 " --> pdb=" O PHE A 344 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N TYR A 368 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL A 387 " --> pdb=" O TYR A 368 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N CYS A 370 " --> pdb=" O LEU A 385 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 480 through 485 removed outlier: 3.691A pdb=" N GLY A 712 " --> pdb=" O ALA A 704 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL A 706 " --> pdb=" O ILE A 710 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ILE A 710 " --> pdb=" O VAL A 706 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 496 through 499 removed outlier: 4.301A pdb=" N VAL A 691 " --> pdb=" O THR A 663 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N LEU A 681 " --> pdb=" O VAL A 694 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 525 through 533 removed outlier: 4.428A pdb=" N SER A 529 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N SER A 515 " --> pdb=" O SER A 529 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N THR A 531 " --> pdb=" O THR A 513 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR A 513 " --> pdb=" O THR A 531 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ILE A 533 " --> pdb=" O ASN A 511 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ASN A 511 " --> pdb=" O ILE A 533 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR A 547 " --> pdb=" O SER A 508 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A 516 " --> pdb=" O ASN A 553 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TYR A 616 " --> pdb=" O VAL A 587 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL A 587 " --> pdb=" O TYR A 616 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLN A 618 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N PHE A 585 " --> pdb=" O GLN A 618 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N THR A 620 " --> pdb=" O SER A 583 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY A 622 " --> pdb=" O SER A 581 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N SER A 581 " --> pdb=" O GLY A 622 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 525 through 533 removed outlier: 4.428A pdb=" N SER A 529 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N SER A 515 " --> pdb=" O SER A 529 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N THR A 531 " --> pdb=" O THR A 513 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR A 513 " --> pdb=" O THR A 531 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ILE A 533 " --> pdb=" O ASN A 511 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ASN A 511 " --> pdb=" O ILE A 533 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR A 547 " --> pdb=" O SER A 508 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A 516 " --> pdb=" O ASN A 553 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LYS A 611 " --> pdb=" O GLY A 602 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N GLY A 602 " --> pdb=" O LYS A 611 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER A 562 " --> pdb=" O TYR A 603 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 744 through 748 Processing sheet with id=AB2, first strand: chain 'A' and resid 778 through 782 Processing sheet with id=AB3, first strand: chain 'A' and resid 785 through 795 removed outlier: 7.071A pdb=" N GLY A1147 " --> pdb=" O ALA A1143 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ALA A1143 " --> pdb=" O GLY A1147 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU A1149 " --> pdb=" O VAL A1141 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL A1141 " --> pdb=" O LEU A1149 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N LEU A1151 " --> pdb=" O SER A1139 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N SER A1139 " --> pdb=" O LEU A1151 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N THR A1153 " --> pdb=" O ILE A1137 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 801 through 803 Processing sheet with id=AB5, first strand: chain 'A' and resid 1217 through 1220 removed outlier: 4.547A pdb=" N ALA A1176 " --> pdb=" O ILE A1220 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 46 through 49 removed outlier: 4.191A pdb=" N TYR B 209 " --> pdb=" O CYS B 227 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 177 through 181 removed outlier: 3.528A pdb=" N GLY B 162 " --> pdb=" O PHE B 173 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 268 through 285 removed outlier: 3.689A pdb=" N LEU B 276 " --> pdb=" O ASN B 442 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASN B 442 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N VAL B 278 " --> pdb=" O SER B 440 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N SER B 440 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N CYS B 280 " --> pdb=" O ILE B 438 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE B 438 " --> pdb=" O CYS B 280 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU B 282 " --> pdb=" O TRP B 436 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TRP B 436 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL B 403 " --> pdb=" O TYR B 410 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 268 through 285 removed outlier: 3.689A pdb=" N LEU B 276 " --> pdb=" O ASN B 442 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASN B 442 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N VAL B 278 " --> pdb=" O SER B 440 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N SER B 440 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N CYS B 280 " --> pdb=" O ILE B 438 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE B 438 " --> pdb=" O CYS B 280 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU B 282 " --> pdb=" O TRP B 436 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TRP B 436 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ASP B 445 " --> pdb=" O TYR B 460 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N TYR B 460 " --> pdb=" O ASP B 445 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU B 447 " --> pdb=" O ILE B 458 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE B 458 " --> pdb=" O LEU B 447 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLU B 449 " --> pdb=" O GLN B 456 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 290 through 295 removed outlier: 6.949A pdb=" N HIS B 335 " --> pdb=" O ASP B 417 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL B 419 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL B 333 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE B 332 " --> pdb=" O PHE B 344 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N TYR B 368 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N VAL B 387 " --> pdb=" O TYR B 368 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N CYS B 370 " --> pdb=" O LEU B 385 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 480 through 485 removed outlier: 3.867A pdb=" N GLY B 712 " --> pdb=" O ALA B 704 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL B 706 " --> pdb=" O ILE B 710 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ILE B 710 " --> pdb=" O VAL B 706 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 496 through 499 removed outlier: 4.286A pdb=" N VAL B 691 " --> pdb=" O THR B 663 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N LEU B 681 " --> pdb=" O VAL B 694 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 525 through 533 removed outlier: 4.447A pdb=" N SER B 529 " --> pdb=" O SER B 515 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N SER B 515 " --> pdb=" O SER B 529 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR B 531 " --> pdb=" O THR B 513 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR B 513 " --> pdb=" O THR B 531 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ILE B 533 " --> pdb=" O ASN B 511 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASN B 511 " --> pdb=" O ILE B 533 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR B 547 " --> pdb=" O SER B 508 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS B 584 " --> pdb=" O THR B 620 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLY B 622 " --> pdb=" O PHE B 582 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N PHE B 582 " --> pdb=" O GLY B 622 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 525 through 533 removed outlier: 4.447A pdb=" N SER B 529 " --> pdb=" O SER B 515 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N SER B 515 " --> pdb=" O SER B 529 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR B 531 " --> pdb=" O THR B 513 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR B 513 " --> pdb=" O THR B 531 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ILE B 533 " --> pdb=" O ASN B 511 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASN B 511 " --> pdb=" O ILE B 533 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR B 547 " --> pdb=" O SER B 508 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N LYS B 611 " --> pdb=" O GLY B 602 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N GLY B 602 " --> pdb=" O LYS B 611 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER B 562 " --> pdb=" O TYR B 603 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 746 through 748 Processing sheet with id=AC7, first strand: chain 'B' and resid 778 through 782 removed outlier: 4.589A pdb=" N LEU B1186 " --> pdb=" O ILE B1166 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 785 through 795 removed outlier: 3.815A pdb=" N PHE B1138 " --> pdb=" O THR B1153 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU B1155 " --> pdb=" O HIS B1136 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N HIS B1136 " --> pdb=" O LEU B1155 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 801 through 803 Processing sheet with id=AD1, first strand: chain 'B' and resid 1217 through 1220 removed outlier: 4.416A pdb=" N ALA B1176 " --> pdb=" O ILE B1220 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU B1230 " --> pdb=" O CYS B1170 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 46 through 51 removed outlier: 4.433A pdb=" N TYR C 223 " --> pdb=" O ASN C 213 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 177 through 181 Processing sheet with id=AD4, first strand: chain 'C' and resid 268 through 285 removed outlier: 5.538A pdb=" N LYS C 269 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL C 450 " --> pdb=" O LYS C 269 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N VAL C 271 " --> pdb=" O ILE C 448 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE C 448 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ASN C 273 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ALA C 446 " --> pdb=" O ASN C 273 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL C 444 " --> pdb=" O PRO C 275 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER C 440 " --> pdb=" O ASN C 279 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU C 281 " --> pdb=" O ILE C 438 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ILE C 438 " --> pdb=" O LEU C 281 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ALA C 283 " --> pdb=" O TRP C 436 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TRP C 436 " --> pdb=" O ALA C 283 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL C 403 " --> pdb=" O TYR C 410 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 268 through 285 removed outlier: 5.538A pdb=" N LYS C 269 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL C 450 " --> pdb=" O LYS C 269 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N VAL C 271 " --> pdb=" O ILE C 448 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE C 448 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ASN C 273 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ALA C 446 " --> pdb=" O ASN C 273 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL C 444 " --> pdb=" O PRO C 275 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER C 440 " --> pdb=" O ASN C 279 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU C 281 " --> pdb=" O ILE C 438 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ILE C 438 " --> pdb=" O LEU C 281 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ALA C 283 " --> pdb=" O TRP C 436 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TRP C 436 " --> pdb=" O ALA C 283 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ASP C 445 " --> pdb=" O TYR C 460 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N TYR C 460 " --> pdb=" O ASP C 445 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU C 447 " --> pdb=" O ILE C 458 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE C 458 " --> pdb=" O LEU C 447 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLU C 449 " --> pdb=" O GLN C 456 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 290 through 295 removed outlier: 3.605A pdb=" N GLN C 292 " --> pdb=" O ILE C 421 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N HIS C 335 " --> pdb=" O ASP C 417 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL C 419 " --> pdb=" O VAL C 333 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL C 333 " --> pdb=" O VAL C 419 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE C 332 " --> pdb=" O PHE C 344 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N TYR C 368 " --> pdb=" O VAL C 387 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL C 387 " --> pdb=" O TYR C 368 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N CYS C 370 " --> pdb=" O LEU C 385 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 480 through 485 removed outlier: 3.647A pdb=" N GLY C 712 " --> pdb=" O ALA C 704 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL C 706 " --> pdb=" O ILE C 710 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ILE C 710 " --> pdb=" O VAL C 706 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 496 through 499 removed outlier: 3.511A pdb=" N GLY C 656 " --> pdb=" O TYR C 649 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL C 691 " --> pdb=" O THR C 663 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N LEU C 681 " --> pdb=" O VAL C 694 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N TYR C 673 " --> pdb=" O LEU C 681 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 525 through 533 removed outlier: 5.440A pdb=" N LEU C 526 " --> pdb=" O GLY C 519 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLY C 519 " --> pdb=" O LEU C 526 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ALA C 528 " --> pdb=" O ALA C 517 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ALA C 517 " --> pdb=" O ALA C 528 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL C 510 " --> pdb=" O THR C 549 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N PHE C 551 " --> pdb=" O VAL C 510 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILE C 512 " --> pdb=" O PHE C 551 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 538 through 540 removed outlier: 5.288A pdb=" N SER C 581 " --> pdb=" O GLY C 622 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY C 622 " --> pdb=" O SER C 581 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR C 620 " --> pdb=" O SER C 583 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N PHE C 585 " --> pdb=" O GLN C 618 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLN C 618 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL C 587 " --> pdb=" O TYR C 616 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TYR C 616 " --> pdb=" O VAL C 587 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 538 through 540 removed outlier: 5.288A pdb=" N SER C 581 " --> pdb=" O GLY C 622 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY C 622 " --> pdb=" O SER C 581 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR C 620 " --> pdb=" O SER C 583 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N PHE C 585 " --> pdb=" O GLN C 618 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLN C 618 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL C 587 " --> pdb=" O TYR C 616 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TYR C 616 " --> pdb=" O VAL C 587 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N LYS C 611 " --> pdb=" O GLY C 602 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLY C 602 " --> pdb=" O LYS C 611 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N SER C 562 " --> pdb=" O TYR C 603 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 744 through 748 Processing sheet with id=AE4, first strand: chain 'C' and resid 778 through 782 Processing sheet with id=AE5, first strand: chain 'C' and resid 785 through 795 removed outlier: 7.010A pdb=" N GLY C1147 " --> pdb=" O ALA C1143 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ALA C1143 " --> pdb=" O GLY C1147 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU C1149 " --> pdb=" O VAL C1141 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL C1141 " --> pdb=" O LEU C1149 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N LEU C1151 " --> pdb=" O SER C1139 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N SER C1139 " --> pdb=" O LEU C1151 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N THR C1153 " --> pdb=" O ILE C1137 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 801 through 803 Processing sheet with id=AE7, first strand: chain 'C' and resid 1217 through 1220 removed outlier: 4.425A pdb=" N ALA C1176 " --> pdb=" O ILE C1220 " (cutoff:3.500A) 996 hydrogen bonds defined for protein. 2697 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.35 Time building geometry restraints manager: 12.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.06 - 1.21: 183 1.21 - 1.36: 8094 1.36 - 1.51: 8447 1.51 - 1.67: 9151 1.67 - 1.82: 138 Bond restraints: 26013 Sorted by residual: bond pdb=" C ASN A 511 " pdb=" O ASN A 511 " ideal model delta sigma weight residual 1.236 1.056 0.180 1.24e-02 6.50e+03 2.11e+02 bond pdb=" C ASN C 422 " pdb=" O ASN C 422 " ideal model delta sigma weight residual 1.232 1.081 0.151 1.12e-02 7.97e+03 1.81e+02 bond pdb=" C ASN A 422 " pdb=" O ASN A 422 " ideal model delta sigma weight residual 1.232 1.103 0.128 1.01e-02 9.80e+03 1.61e+02 bond pdb=" CA ASN B 422 " pdb=" CB ASN B 422 " ideal model delta sigma weight residual 1.527 1.432 0.096 7.60e-03 1.73e+04 1.58e+02 bond pdb=" C ASN C 511 " pdb=" O ASN C 511 " ideal model delta sigma weight residual 1.235 1.102 0.132 1.18e-02 7.18e+03 1.26e+02 ... (remaining 26008 not shown) Histogram of bond angle deviations from ideal: 80.67 - 92.04: 13 92.04 - 103.41: 389 103.41 - 114.78: 15083 114.78 - 126.15: 19389 126.15 - 137.52: 571 Bond angle restraints: 35445 Sorted by residual: angle pdb=" N ASN B 723 " pdb=" CA ASN B 723 " pdb=" C ASN B 723 " ideal model delta sigma weight residual 113.20 127.33 -14.13 1.21e+00 6.83e-01 1.36e+02 angle pdb=" N ASN C 723 " pdb=" CA ASN C 723 " pdb=" C ASN C 723 " ideal model delta sigma weight residual 113.18 126.88 -13.70 1.21e+00 6.83e-01 1.28e+02 angle pdb=" N ASN A 723 " pdb=" CA ASN A 723 " pdb=" C ASN A 723 " ideal model delta sigma weight residual 113.02 125.75 -12.73 1.20e+00 6.94e-01 1.13e+02 angle pdb=" N ASN B 348 " pdb=" CA ASN B 348 " pdb=" CB ASN B 348 " ideal model delta sigma weight residual 110.32 92.41 17.91 1.70e+00 3.46e-01 1.11e+02 angle pdb=" N ASN C 685 " pdb=" CA ASN C 685 " pdb=" C ASN C 685 " ideal model delta sigma weight residual 108.20 91.78 16.42 1.71e+00 3.42e-01 9.22e+01 ... (remaining 35440 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.12: 15562 24.12 - 48.24: 666 48.24 - 72.35: 113 72.35 - 96.47: 44 96.47 - 120.59: 10 Dihedral angle restraints: 16395 sinusoidal: 7128 harmonic: 9267 Sorted by residual: dihedral pdb=" N ASN B 348 " pdb=" C ASN B 348 " pdb=" CA ASN B 348 " pdb=" CB ASN B 348 " ideal model delta harmonic sigma weight residual 122.80 99.57 23.23 0 2.50e+00 1.60e-01 8.64e+01 dihedral pdb=" N ASN A 213 " pdb=" C ASN A 213 " pdb=" CA ASN A 213 " pdb=" CB ASN A 213 " ideal model delta harmonic sigma weight residual 122.80 145.66 -22.86 0 2.50e+00 1.60e-01 8.36e+01 dihedral pdb=" C ASN A 213 " pdb=" N ASN A 213 " pdb=" CA ASN A 213 " pdb=" CB ASN A 213 " ideal model delta harmonic sigma weight residual -122.60 -145.02 22.42 0 2.50e+00 1.60e-01 8.04e+01 ... (remaining 16392 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.868: 4364 0.868 - 1.736: 24 1.736 - 2.605: 14 2.605 - 3.473: 11 3.473 - 4.341: 3 Chirality restraints: 4416 Sorted by residual: chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 0.80 -3.20 2.00e-02 2.50e+03 2.55e+04 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 0.35 -2.75 2.00e-02 2.50e+03 1.90e+04 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.12 -2.28 2.00e-02 2.50e+03 1.30e+04 ... (remaining 4413 not shown) Planarity restraints: 4473 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1412 " -0.414 2.00e-02 2.50e+03 3.35e-01 1.40e+03 pdb=" C7 NAG A1412 " 0.119 2.00e-02 2.50e+03 pdb=" C8 NAG A1412 " -0.223 2.00e-02 2.50e+03 pdb=" N2 NAG A1412 " 0.568 2.00e-02 2.50e+03 pdb=" O7 NAG A1412 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1427 " 0.398 2.00e-02 2.50e+03 3.19e-01 1.28e+03 pdb=" C7 NAG B1427 " -0.117 2.00e-02 2.50e+03 pdb=" C8 NAG B1427 " 0.231 2.00e-02 2.50e+03 pdb=" N2 NAG B1427 " -0.533 2.00e-02 2.50e+03 pdb=" O7 NAG B1427 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1401 " 0.368 2.00e-02 2.50e+03 3.15e-01 1.24e+03 pdb=" C7 NAG B1401 " -0.090 2.00e-02 2.50e+03 pdb=" C8 NAG B1401 " 0.052 2.00e-02 2.50e+03 pdb=" N2 NAG B1401 " -0.549 2.00e-02 2.50e+03 pdb=" O7 NAG B1401 " 0.219 2.00e-02 2.50e+03 ... (remaining 4470 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.05: 12 2.05 - 2.76: 2045 2.76 - 3.48: 34642 3.48 - 4.19: 58657 4.19 - 4.90: 103744 Nonbonded interactions: 199100 Sorted by model distance: nonbonded pdb=" OD2 ASP B 431 " pdb=" O6 NAG J 1 " model vdw 1.341 3.040 nonbonded pdb=" OD2 ASP B 431 " pdb=" C6 NAG J 1 " model vdw 1.602 3.440 nonbonded pdb=" OD2 ASP A 431 " pdb=" O6 NAG E 1 " model vdw 1.603 3.040 nonbonded pdb=" OD2 ASP A 431 " pdb=" C6 NAG E 1 " model vdw 1.743 3.440 nonbonded pdb=" OG SER C1139 " pdb=" ND1 HIS C1152 " model vdw 1.826 3.120 ... (remaining 199095 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.070 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 81.770 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 0.180 26013 Z= 1.122 Angle : 2.301 28.058 35445 Z= 1.386 Chirality : 0.273 4.341 4416 Planarity : 0.028 0.335 4419 Dihedral : 14.729 120.591 10344 Min Nonbonded Distance : 1.341 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.66 % Allowed : 5.65 % Favored : 91.68 % Cbeta Deviations : 2.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.13), residues: 3150 helix: -2.24 (0.16), residues: 615 sheet: 0.71 (0.20), residues: 618 loop : -1.01 (0.13), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.112 0.023 TRP B 165 HIS 0.011 0.004 HIS A 507 PHE 0.074 0.015 PHE B 408 TYR 0.162 0.025 TYR C 950 ARG 0.013 0.002 ARG C1210 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 489 time to evaluate : 2.811 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 HIS cc_start: 0.7496 (m-70) cc_final: 0.7010 (m-70) REVERT: A 290 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8326 (pt) REVERT: A 322 ASP cc_start: 0.7563 (t0) cc_final: 0.7266 (t0) REVERT: A 583 SER cc_start: 0.8680 (t) cc_final: 0.8257 (p) REVERT: A 679 GLN cc_start: 0.7546 (tt0) cc_final: 0.7182 (tp40) REVERT: A 737 ASP cc_start: 0.7684 (t0) cc_final: 0.7396 (t0) REVERT: A 745 VAL cc_start: 0.8814 (m) cc_final: 0.8586 (t) REVERT: A 867 ASP cc_start: 0.7338 (t70) cc_final: 0.6786 (t0) REVERT: A 933 SER cc_start: 0.8642 (m) cc_final: 0.8177 (p) REVERT: A 935 VAL cc_start: 0.9000 (p) cc_final: 0.8542 (m) REVERT: A 994 GLN cc_start: 0.7514 (mm-40) cc_final: 0.7140 (mm110) REVERT: A 1068 TYR cc_start: 0.8403 (m-80) cc_final: 0.7989 (m-80) REVERT: A 1135 GLU cc_start: 0.7005 (mm-30) cc_final: 0.6776 (mm-30) REVERT: A 1175 ILE cc_start: 0.8031 (pt) cc_final: 0.6700 (pt) REVERT: B 209 TYR cc_start: 0.7811 (m-80) cc_final: 0.7534 (m-10) REVERT: B 234 TYR cc_start: 0.7574 (t80) cc_final: 0.7246 (t80) REVERT: B 450 VAL cc_start: 0.8433 (t) cc_final: 0.8200 (m) REVERT: B 566 ASP cc_start: 0.7464 (t0) cc_final: 0.7209 (t0) REVERT: B 578 ASP cc_start: 0.7790 (t0) cc_final: 0.7340 (t70) REVERT: B 583 SER cc_start: 0.8626 (t) cc_final: 0.8308 (p) REVERT: B 588 SER cc_start: 0.8505 (t) cc_final: 0.8130 (t) REVERT: B 599 ASP cc_start: 0.7441 (m-30) cc_final: 0.7223 (m-30) REVERT: B 635 ILE cc_start: 0.8855 (mm) cc_final: 0.8651 (mt) REVERT: B 641 MET cc_start: 0.8200 (mtm) cc_final: 0.7964 (mtt) REVERT: B 809 VAL cc_start: 0.8504 (t) cc_final: 0.8168 (m) REVERT: B 815 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8106 (tpp-160) REVERT: B 851 ILE cc_start: 0.8459 (mp) cc_final: 0.8234 (mm) REVERT: B 867 ASP cc_start: 0.7695 (t0) cc_final: 0.7212 (t0) REVERT: B 913 ASP cc_start: 0.7904 (p0) cc_final: 0.7589 (p0) REVERT: B 933 SER cc_start: 0.8617 (m) cc_final: 0.8262 (p) REVERT: B 994 GLN cc_start: 0.7592 (tm-30) cc_final: 0.7166 (tp40) REVERT: B 1135 GLU cc_start: 0.7036 (mm-30) cc_final: 0.6781 (mm-30) REVERT: C 450 VAL cc_start: 0.8232 (t) cc_final: 0.8008 (m) REVERT: C 568 ASN cc_start: 0.7641 (t160) cc_final: 0.7410 (t0) REVERT: C 578 ASP cc_start: 0.7446 (t70) cc_final: 0.6998 (t0) REVERT: C 583 SER cc_start: 0.8809 (t) cc_final: 0.8608 (p) REVERT: C 867 ASP cc_start: 0.7435 (t70) cc_final: 0.6991 (t0) REVERT: C 994 GLN cc_start: 0.7062 (mm-40) cc_final: 0.6677 (mm-40) REVERT: C 1007 ILE cc_start: 0.7831 (pt) cc_final: 0.7599 (mm) REVERT: C 1041 SER cc_start: 0.8074 (m) cc_final: 0.7872 (t) REVERT: C 1065 ASP cc_start: 0.7484 (OUTLIER) cc_final: 0.7132 (t0) REVERT: C 1135 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6991 (mm-30) outliers start: 73 outliers final: 32 residues processed: 547 average time/residue: 0.3199 time to fit residues: 283.3592 Evaluate side-chains 351 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 316 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 341 ASN Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 1145 PRO Chi-restraints excluded: chain A residue 1241 ASP Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 341 ASN Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 505 ASN Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain B residue 723 ASN Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 1145 PRO Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 297 ASN Chi-restraints excluded: chain C residue 341 ASN Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 723 ASN Chi-restraints excluded: chain C residue 902 VAL Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain C residue 1065 ASP Chi-restraints excluded: chain C residue 1154 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 0.5980 chunk 241 optimal weight: 0.9980 chunk 133 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 162 optimal weight: 0.5980 chunk 128 optimal weight: 0.7980 chunk 249 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 151 optimal weight: 0.6980 chunk 185 optimal weight: 0.5980 chunk 288 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: